corrected handling of STDIN|STDOUT
adopted ASCII_TABLE class
This commit is contained in:
Philip Eisenlohr
parent
267b8ac30c
commit
18a09d7cff
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@ -1,6 +1,6 @@
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#!/usr/bin/python
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import os,re,sys,math,numpy,string
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import os,re,sys,math,numpy,string,damask_tools
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from optparse import OptionParser, Option
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# -----------------------------
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@ -22,13 +22,6 @@ class extendableOption(Option):
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Option.take_action(self, action, dest, opt, value, values, parser)
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def prefixMultiply(what,len):
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return {True: ['%i_%s'%(i+1,what) for i in range(len)],
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False:[what]}[len>1]
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# --------------------------------------------------------------------
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# MAIN
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@ -42,14 +35,11 @@ deformation gradient and first Piola--Kirchhoff stress.
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)
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parser.add_option('-m','--memory', dest='memory', action='store_true', \
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help='load complete file into memory [%default]')
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parser.add_option('-f','--defgrad', dest='defgrad', type='string', \
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help='heading of columns containing deformation gradient [%default]')
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parser.add_option('-p','--stress', dest='stress', type='string', \
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help='heading of columns containing first Piola--Kirchhoff stress [%default]')
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parser.set_defaults(memory = False)
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parser.set_defaults(defgrad = 'f')
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parser.set_defaults(stress = 'p')
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@ -74,7 +64,7 @@ datainfo['stress']['label'].append(options.stress)
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files = []
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if filenames == []:
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files.append({'name':'STDIN', 'handle':sys.stdin})
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files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
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else:
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for name in filenames:
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if os.path.exists(name):
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@ -83,30 +73,12 @@ else:
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# ------------------------------------------ loop over input files ---------------------------------------
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for file in files:
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print file['name']
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if file['name'] != 'STDIN': print file['name']
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# get labels by either read the first row, or - if keyword header is present - the last line of the header
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firstline = file['input'].readline()
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m = re.search('(\d+)\s*head', firstline.lower())
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if m:
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headerlines = int(m.group(1))
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passOn = [file['input'].readline() for i in range(1,headerlines)]
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headers = file['input'].readline().split()
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else:
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headerlines = 1
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passOn = []
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headers = firstline.split()
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if options.memory:
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data = file['input'].readlines()
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else:
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data = []
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for i,l in enumerate(headers):
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if l.startswith('1_'):
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if re.match('\d+_',l[2:]) or i == len(headers)-1 or not headers[i+1].endswith(l[2:]):
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headers[i] = l[2:]
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table = damask_tools.ASCII_TABLE(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace('$Id$','\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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active = {}
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column = {}
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@ -116,56 +88,38 @@ for file in files:
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for label in info['label']:
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key = {True :'1_%s',
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False:'%s' }[info['len']>1]%label
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if key not in headers:
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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active[datatype].append(label)
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column[datatype][label] = headers.index(key)
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head += prefixMultiply('Cauchy',datainfo[datatype]['len'])
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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table.labels_append(['%i_Cauchy'%(i+1)
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for i in xrange(datainfo['defgrad']['len'])]) # extend ASCII header with new labels
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# ------------------------------------------ assemble header ---------------------------------------
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output = '%i\theader'%(headerlines+1) + '\n' + \
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''.join(passOn) + \
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string.replace('$Id$','\n','\\n')+ '\t' + \
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' '.join(sys.argv[1:]) + '\n' + \
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'\t'.join(headers + head) + '\n' # build extended header
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table.head_write()
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if not options.memory:
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file['output'].write(output)
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output = ''
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# ------------------------------------------ process data ---------------------------------------
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# ------------------------------------------ read file ---------------------------------------
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while table.data_read(): # read next data line of ASCII table
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for line in {True : data,
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False : file['input']}[options.memory]:
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items = line.split()[:len(headers)]
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if len(items) < len(headers):
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continue
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F = numpy.array(map(float,table.data[column['defgrad'][active['defgrad'][0]]:
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column['defgrad'][active['defgrad'][0]]+datainfo['defgrad']['len']]),'d').reshape(3,3)
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P = numpy.array(map(float,table.data[column['stress'][active['stress'][0]]:
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column['stress'][active['stress'][0]]+datainfo['stress']['len']]),'d').reshape(3,3)
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output += '\t'.join(items)
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F = numpy.array(map(float,items[column['defgrad'][active['defgrad'][0]]:
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column['defgrad'][active['defgrad'][0]]+datainfo['defgrad']['len']]),'d').reshape(3,3)
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P = numpy.array(map(float,items[column['stress'][active['stress'][0]]:
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column['stress'][active['stress'][0]]+datainfo['stress']['len']]),'d').reshape(3,3)
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output += '\t'+'\t'.join(map(str,1.0/numpy.linalg.det(F)*numpy.dot(P,F.T).reshape(9))) # [Cauchy] = (1/det(F)) * [P].[F_transpose]
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output += '\n'
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if not options.memory:
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file['output'].write(output)
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output = ''
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file['input'].close()
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table.data_append(list(1.0/numpy.linalg.det(F)*numpy.dot(P,F.T).reshape(9))) # [Cauchy] = (1/det(F)) * [P].[F_transpose]
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table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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if options.memory:
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file['output'].write(output)
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table.output_flush() # just in case of buffered ASCII table
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file['input'].close() # close input ASCII table
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if file['name'] != 'STDIN':
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file['output'].close
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os.rename(file['name']+'_tmp',file['name'])
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file['output'].close # close output ASCII table
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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